First, you really should be doing a parallel export-import for a database of this size. The downtime window will kill you otherwise.
I recently did a MSCS cluster migration to HANA and we did have this problem on one run. It was due to a very large RS table that wasn't split correctly. Table splitting can kill you.
So go back and look at your table split, look at the details of which tables are importing slowly (you can see this in the logs). Check all your kernels, disp+work, SAP HANA Clients, r3load and libdbsql are all on the VERY LATEST versions.